Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

High-Risk Human Papillomavirus Infection in Squamous Cell Carcinoma of the Larynx: A Study From a Tertiary Care Center in North India.

Background Human papillomavirus (HPV) 16/18 infection has been considered as an important etiological factor for laryngeal carcinoma. Considering its impact on prognosis, it is important to understand the true prevalence of HPV-associated laryngeal squamous cell carcinoma (LSCC) in the northeast region of India. Materials and methods A prospective observational study was conducted among patients with laryngeal squamous cell carcinoma in the department of otolaryngology of King George's Medical University (KGMU), Lucknow. Results In this study, the total number of cases was 62. HPV 16/18 positivity was higher (p=0.02) among the age group 31-40 years (40%) as compared to above 50 years (3.3%). HPV positivity was higher among females (50%) as compared to males (12.5%). Out of 34 tobacco smokers, HPV positivity was seen in 20.6% as compared to no positivity among patients without any history of addiction. HPV positivity was found in 19.6% of supraglottic cancer and no positivity among glottic cancer. HPV positivity was higher among the T1 stage of supraglottic carcinoma (40%) as compared to T3 (17.4%). In glottic cases, HPV positivity was nil in all T stages. Conclusion The association of tumor HPV status with laryngeal squamous cell carcinoma in females and young patients (<50 years) observed in our study is consistent with prior studies, and this reflects that HPV status should be considered in the design or analysis for the treatment of laryngeal cancer. We tried to highlight the importance of diagnosing HPV-positive laryngeal squamous cell carcinoma at early stages of the disease and also added information about the prevalence of HPV-positive LSCC in this zone of the country. We have observed that laryngeal carcinoma from tobacco smokers contains transcriptionally active HPV and hence may act as a risk factor or act synergistically with HPV infection. Further studies with larger sample size are needed to clearly establish the association of HPV in laryngeal squamous cell carcinoma and its impact on disease prognosis.

Effect of synthetic and aromatic amine antioxidants on oxidation stability, performance, and emission analysis of waste cooking oil biodiesel.

In the present study, an attempt was made to improve the oxidation stability of biodiesel by adding antioxidants to waste cooking oil biodiesel, and their impact on performance and emissions was analyzed. Two types of antioxidants were chosen for the analysis: an aromatic amine antioxidant, diphenylamine (DPA), and synthetic oxidants, tert-butylhydroxyquinone (TBHQ) and pyrogallol (PY). All the antioxidants were added to the biodiesel at doses of 200 ppm and 500 ppm to evaluate their effect. The oxidation stability was found as per the ASTM standard by mixing 500 ppm antioxidants for all three antioxidant-treated biodiesel blends. DPA yielded similar results as TBHQ, although PY had a better oxidation stability according to the Rancimat test. Gas chromatography and mass chromatography were also performed on the neat biodiesel. Performance and emission tests were performed on the antioxidant-treated biodiesel blends and diesel. The brake thermal efficiency of the tested fuel increased by 9.8%, 6.9%, and 15.88% when the DPA, TBHQ, and PY antioxidants were added to the test fuel compared to that of the test fuel without added antioxidant. The brake specific energy consumption of the test fuel decreased by 9.05% with DPA, 7.03% with TBHQ, and 14.08% with PY compared to that of the test fuel without antioxidant. The NOx emissions of the antioxidant-treated test fuels were reduced by 14.65% with DPA, 11.22% with TBHQ, and 23.10% with PY compared to those of the test fuel without antioxidants. Additionally, the aromatic amine antioxidant (DPA) was found to be effective in enhancing the performance and lowering the exhaust emissions compared to diesel for unmodified diesel engines.

Parental and staff experiences of restricted parental presence on a Neonatal Intensive Care Unit during COVID-19.

AIM: The COVID-19 pandemic had a significant impact on parental presence in the Neonatal Intensive Care Unit (NICU) during the first wave. The NICU team at the Rosie Hospital, Cambridge, endeavoured to explore the impact on parent and staff experiences of supporting parents throughout the period when visiting was restricted, between 13th August and 11th September 2020. METHODS: Bespoke surveys were designed following the first lockdown to gather information on the impact on staff and parents. The questions were developed in the context of initial observations and conversations with staff and parents. RESULTS: The findings of this study have illustrated the extent of the restrictions on parental wellbeing and mood, with the restrictions having had an adverse effect on these. In addition, the findings illustrate the adverse effect that the parents reported due to the restricted presence in terms of their babies' wellbeing, parent-infant bonding, partners' wellbeing, parental confidence, the ability to breastfeed confidently and parents' access to the medical teams. CONCLUSION: The findings of this study have a number of clinical implications for parents and staff. Namely, the data supported the decision not to close NICU again during the second and third waves.

Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.

The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.

Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance.

It is important to improve the understanding of the interactions between the trees and pathogens and integrate this knowledge about disease resistance into tree breeding programs. The conifer Norway spruce (Picea abies) is an important species for the forest industry in Europe. Its major pathogen is Heterobasidion parviporum, causing stem and root rot. In this study, we identified 11 Norway spruce QTLs (Quantitative trait loci) that correlate with variation in resistance to H. parviporum in a population of 466 trees by association genetics. Individual QTLs explained between 2.1 and 5.2% of the phenotypic variance. The expression of candidate genes associated with the QTLs was analysed in silico and in response to H. parviporum hypothesizing that (a) candidate genes linked to control of fungal sapwood growth are more commonly expressed in sapwood, and; (b) candidate genes associated with induced defences are respond to H. parviporum inoculation. The Norway spruce laccase PaLAC5 associated with control of lesion length development is likely to be involved in the induced defences. Expression analyses showed that PaLAC5 responds specifically and strongly in close proximity to the H. parviporum inoculation. Thus, PaLAC5 may be associated with the lignosuberized boundary zone formation in bark adjacent to the inoculation site.

Active versus passive cooling during neonatal transport.

BACKGROUND AND OBJECTIVE: Therapeutic hypothermia is now the standard of care for hypoxic-ischemic encephalopathy. Treatment should be started early, and it is often necessary to transfer the infant to a regional NICU for ongoing care. There are no large studies reporting outcomes from infants cooled passively compared with active (servo-controlled) cooling during transfer. Our goal was to review data from a regional transport service, comparing both methods of cooling. METHODS: This was a retrospective observational study of 143 infants referred to a regional NICU for ongoing therapeutic hypothermia. Of the 134 infants transferred, the first 64 were cooled passively, and 70 were subsequently cooled after purchase of a servo-controlled mattress. Key outcome measures were time to arrival at the regional unit, temperature at referral and arrival at the regional unit, and temperature stability during transfer. RESULTS: The age cooling was started was significantly shorter in the actively cooled group (46 [0-352] minutes vs 120 [0-502] minutes; P <.01). The median (range) stabilization time (153 [60-385] minutes vs 133 [45-505] minutes; P = .04) and age at arrival at the regional unit (504 [191-924] minutes vs 452 [225-1265]) minutes; P = .01) were significantly shorter in the actively cooled group. Only 39% of infants passively cooled were within the target temperature range at arrival to the regional unit compared with 100% actively cooled. CONCLUSIONS: Servo-controlled active cooling has been shown to improve temperature stability and is associated with a reduction in transfer time.

Endotracheal intubation in a neonatal population remains associated with a high risk of adverse events.

INTRODUCTION: There has been a significant increase in premedication use for neonatal intubation in the UK over the past decade. We aimed to determine the adverse events during neonatal intubation using the most commonly used premedication regimen in the UK. DISCUSSION: We prospectively studied all intubations performed using morphine, suxamethonium and atropine during a 3-month period in three UK tertiary neonatal units. Premedication was administered for 87/93 (94%) of intubations. Median time taken to prepare premedication was 16 min (IQR 10-35). Median time to successful intubation was 5 min (IQR 2-9) following premedication. Median lowest recorded oxygen saturation after administration of premedication was 65% (IQR 39-85). A bradycardia in the range 61-99/min accompanied the procedure in 24/93 (26%) intubations, with a median duration of bradycardia of 8 s (IQR 1-10). CONCLUSION: Despite the widespread move to premedication for neonatal intubation, many deficiencies in everyday practice remain. The rate of haemodynamic complications is high in this commonly used premedication regimen. This study shows that there are important factors to control at the local level in terms of timely preparation and administration of premedication drugs, training and supervision of staff carrying out this high-risk procedure.

Use of premedication for intubation in tertiary neonatal units in the United Kingdom.

BACKGROUND: Endotracheal intubation and laryngoscopy are frequently performed procedures in neonatal intensive care. These procedures represent profoundly painful stimuli and have been associated with laryngospasm, bronchospasm, hemodynamic changes, raised intracranial pressure and an increased risk of intracranial hemorrhage. These adverse changes can cause significant neonatal morbidity but may be attenuated by the use of suitable premedication. AIMS: To evaluate current practices for premedication use prior to elective intubation in UK tertiary neonatal units. METHODS: Telephone questionnaire survey of all 50 tertiary neonatal units in the UK. RESULTS: Ninety percent of units report the routine use of sedation prior to intubation and 82% of units routinely use a muscle relaxant. Morphine was the most commonly used sedative and suxamethonium was the most commonly used muscle relaxant. Approximately half of the units also used atropine during intubation. Seventy seven percent of units had a written policy for premedication. Ten percent of the units did not routinely use any sedatives or muscle relaxants for elective intubation. CONCLUSIONS: In comparison with data from a 1998 survey, our study demonstrated an increase in the number of units that have adopted a written policy for premedication use, and in the number routinely using premedication drugs for elective intubation. There remains little consensus as to which drugs should be used and in what dose.